Hi Sunita,
I believe this is because the residue name to be used by LEaP is defined in
atomic_ions.lib. Try changing Mg2+ for MG, and let us know if that works.
Cheers,
El mié., 25 mar. 2020 a las 15:13, Sunita Patel (<sunita.patel.cbs.ac.in>)
escribió:
> Dear Amber Users,
>
> I am generating the coordinate and topology files. My initial structure is
> a protein bound to DNA and two Mg2+ ions. When I am running tleap I am
> getting the error Mg2 does not have a type. I checked the
> "leaprc.water.tip3p" file which shows atom type of Mg2+. Then, why am I
> getting this error.
>
> I am stuck because of this problem.
> Your help will be highly appreciated.
>
> Sincerely,
> Sunita
>
> -------------------------------------------------------
> /home/external/cbs/sunitap/softwares/amber18/bin/teLeap: Warning!
> -no luck
> Added missing heavy atom: .R<CGLN 123>.A<OXT 18>
> Creating new UNIT for residue: Mg sequence: 148
> Created a new atom named: Mg2 within residue: .R<Mg 148>
> Creating new UNIT for residue: Mg sequence: 149
> Created a new atom named: Mg2 within residue: .R<Mg 149>
> total atoms in file: 1249
> Leap added 1030 missing atoms according to residue templates:
> 1 Heavy
> 1029 H / lone pairs
> The file contained 2 atoms not in residue templates
> Checking Unit.
>
> /home/external/cbs/sunitap/softwares/amber18/bin/teLeap: Warning!
> The unperturbed charge of the unit (-22.000000) is not zero.
> FATAL: Atom .R<Mg 148>.A<Mg2 1> does not have a type.
> FATAL: Atom .R<Mg 149>.A<Mg2 1> does not have a type.
>
> /home/external/cbs/sunitap/softwares/amber18/bin/teLeap: Fatal Error!
> Failed to generate parameters
>
> Exiting LEaP: Errors = 1; Warnings = 5; Notes = 1.
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--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Wed Mar 25 2020 - 08:00:02 PDT
